Although Confucianism had been adopted as "orthodox" state doctrine since the Han period 漢, and Neo-Confucianism since the Yuan period 元, there existed many liberate and oppositional ways of thought among the Ming Confucian scholarship, especially among the scholars of the Donglin Academy 東林院. Daoism and Chan Buddhism showed their influence in the thinking of Ming scholars that retired from official posts and developed quietistic philosophies that were more oriented to the own person and the place of humans in the universe than to construct an ideal state like the pre-Han philosophers had done.

Song Lian 宋濂 (1310-1381) undertook the compilation of the official dynastic history (zhengshi 正史) of the Yuan period, Yuanshi 元史. He was also one of the first Yuan scholars that were employed as expert personnel by the founder of the Ming dynasty. Although he was an adherent of Zhu Xi's philosophy his thoughts clearly show deeper influences of Buddhist and Daoist thought than that of the great Southern Song Neo-Confucian master Zhu Xi. It is not enough to study only the Confucian writings, he said, but a good scholar also should broaden his knowledge by investigating the teachings of the Buddhists and Daoists, because their writings all influenced later Confucian thought, and are therefore able to "enlighten the mind and to make clear the human character" (ming xin jian xing 明心見性). Song Lian's writings are assembled in the collections "Collected Writings from Luoshan" Luoshanji 蘿山集 and Qianxiji 潛溪集 "Collected Writings from Recluse Creek".Fang Xiaoru 方孝儒 (1357-1402), although a disciple of Song Lian, refused to consider the relevance of Buddhist thoughts in Neo-Confucian philosophy. For him, both the study of the traditional writings, as well as the practical reference of philosophy, were important (bo wen yi zhi qi zhi, zhu jing yi du qi xing 博文以致其知，主敬以篤其行 "Have a vast [knowledge] in literature to your learning; make respect your master to consolidate your practice."). Fang Xiaoru was later arrested and executed for political reasons.
Cao Duan 曹端 (1376-1434), Xue Xuan 薛瑄 (1389-1464), Wu Yubi 吳與弼 (1391-1469), Hu Juren 胡居仁 (1434-1484).

The first two purely Ming Neo-Confucian philosophers are Chen Xianzhang 陳獻章 (1428-1500) and Zhan Ruoshui 湛若水 (1466-1560).Chen Xianzhang 陳獻章 tought that is not necessary to study an endless number of theories and objects but that the truth of the universal principle is laid down in one's own heart and can be found there in one-self ("look for [the truth] in my own mind" qiu zhi wu xin 求之吾心; "obtain [the truth] from youself"zi de 自得). A method to obtain the universal truth is quietness ("meditation" jing zuo 靜坐) and the concentration to search out the "begin of the fathom" (xun jian duan xu 尋見端緒; "nourish the begin in quietness" jing yang duan ni 靜養端倪) of this world of confusion, and to make oneself free of impure disturbances. True knowledge found in one's mind (xin 心) encompasses the whole world without separating large from small, or inner from outer. Although these ideas reflect the teachings of Lu Jiuyuan, Chen Xianzhang does not explicitly rely on this proponent of Southern Song Neo-Confucianism. Chen's writings are found in the Baishazi quanji 白沙子全集 "Collection of Master White Sand".Zhan Ruoshi's 湛若水 ideas are manifested in his many commentaries to the Confucian Clasics, as well as in the Ganquan xiansheng wenji 甘泉先生文集 "Collection of Master Sweet-Well". He was a friend of the great philosopher Wang Shouren who shared a common view of the inherent good principle of nature that can be intuitively perceived everywhere and in every human being ("suichu tiren tianli" 隨處體認天理). But unlike Chen Xianzhang, Zhan Ruoshi did not discard studying the writings of the old masters in favour of going back to "nature, our ancestor" (yi ziran wei zong 以自然為宗). For Zhan Ruoshui both acting and non-acting, both practice and theory were relevant for unveiling the truth of natural order. Because all activities are expression of the universal order, moving and pausing are one and the same. The human character is a singular expression of the universal mind, in his purest expression, the four Confucian virtues of humanity, righteousness, ritual and wisdom. Although Zhan Ruoshi assumes that the universal order or principle is inherent in everything and everybody he goes not as far as Wang Shouren who stressed that it is not necessary to investigate too many things.

The greatest Ming philospher is Wang Yangming 王陽明 (Wang Shouren 王守仁; 1472-1528; Yangming is the name of his study) who created an anti-intellectual thought by combining the Neo-Confucian theory of a universal order (li 理 or tianli 天理) that is given by nature to every human being with Mencius' (Mengzi 孟子) philosophy of natural goodness of man. An innate knowledge (liangzhi 良知) thus enables man to reach the state of perfection or that of a "gentleman" (junzi 君子) even without learning or studying the Confucian Classics.
Wang Yangming was not a philosopher by profession, he was a typical state offical that served in several high civil as well as military positions. From 1506-1510 he was exiled in a small town in Guizhou province named Longchang 龍場. Here he experienced a change in thoughts and was converted from a traditional adherent of the teachings of the orthodox Neo-Confucian Zhu Xi 朱熹 ("teaching of the universal order" lixue 理學) to a disciple of of "teaching of the mind" (xinxue 心學) founded by Lu Jiuyuan 陸九淵. In Wang Shouren's eyes Zhu Xi and his adherents lacked the idea of unity of cosmic order. Under the influence of Buddhism and Daoism Wang Shouren exploited the concept that moving and pausing, knowledge and acting cannot be separated from each other but rather shape an inseparable unit. He followed the concept of Lu Jiuyuan who defined each man's mind (xin 心) as identical with the universal order. This universal order is given to man by nature and can be thoroughly perceived by self-discipline that ultimately results in innate knowledge of what is good for man according to the universal order and what not. Innate knowledge as identical with the universal order is originary and totally pure. By birth all men are therefore one single body ("the ten thousand beings are one single body" wan wu yi ti 萬物一體) and united with the cosmic principle of goodness. It is therefore enough to study goodness - and therewith the cosmic principle or universal order - in one single detail, in one single person, eventually one's one self, or with the words of Mengzi, "all ten thousand beings are laid down in me" (wan wu jie bei yu wo 萬物皆備於我). For Zhu Xi, studing as much things as possible ("to measure things" ge wu 格物), especially the Confucian Classics, was necessary to obtain knowledge ("investigate things to search for knowledge" ji wu qiu zhi 即物求知). This pharisaism rather leads, as Wang Shouren explains in his critique, to false erudition and to quarrels about minuscule problems instead of leading to knowledge (zhi zhi 致知). While Zhu Xi emphasized that knowledges comes before action (zhi xian xing hou 知先行後), Wang Shouren brings up the concept that knowledge and action are one inseparable unit (zhi xing he yi 知行合一). True uprightness (cheng 誠) will help man to promote goodness, to correct false behaviour ("to correct things" ge wu 格物) and finally to become a perfect man (junzi 君子). Knowledge will necessarily lead to right behaviour, and right behaviour expresses the knowledge of what is good according to the universal principle. Man's character (xing 性) is, although it might be expressed quite different in different persons, identical with the natural principle, it is the pivot between the natural order and the mind. Like all man have an innate Buddha-nature, Wang Shouren assumes that everybody is able to become a perfect man. Different characters are only a different expression of the universal principle. Respecting parents and elderly persons, basic rules of Confucianism, are given to man because he is man, loyalty and benevolence are mutual attitudes that are not leart but are natural by birth, from "Primary Heaven" (xiantian 先天). Behaviour and knowledge are therefore identical, and man has only to "illuminate the luminating virtue" (ming ming de 明明德) of natural order, as the classic Daxue 大學 says.
Li Zhi 李贄 even renounces the orthodox Confucianism and accuses his contemporarians of pharisaism. He sympathized with Buddhism and vernacular literature of the urban population, and he acted as advocate of discriminated and disadvantaged groups like the poor average people, women and ethnic minorities.

Science and Knowledge

In the field of scientific literature, Mei Yingzu 梅膺祚 was the first to develop the modern 214 character radicals in his dictionary Zihui 字彙 (an not, as often can be read, the authors of the Kangxi zidian 康熙字典). Numerous publications about geography - also of foreign countries, techniques, agronomy, geologycraftsmanship, military, medicine and pharmakology were published, for example Chen Fu's 陳旉 and Wang Zhen's 王禎 Nongshu 農書 "Book of Agronomy", Xu Guangqi's 徐光啟 agronomic encyclopedia Nongzheng quanshu 農政全書, and Li Shizhen's 李時珍 pharmakological encyclopedia Bencao gangmu 本草綱目. Another interesting book is the illustrated encyclopedia Sancai tuhui 三才圖會 "Assembled illustrations of the three realms of Heaven, Earth and Man". At the end of Ming, Jesuit missionaries translated Western writings (and not only the Bible!, Chinese: Shengjing 聖經), and Chinese writers described machines the Jesuits had presented to the Chinese Emperors. Like today, the Chinese scholars of late Ming Dynasty were especially interested in science and technique of the West. But Western missionaries and travelers also brought Chinese science to Europe.

Anecdotes, Stories and Novels
The advance in printing technique as well as the demand from an urban public made it necessary and possible for vernacular literature to become more widespread than ever before. Anecdotes, stories and tales were published in collections like Pai'an iingqi 拍案驚奇 "Surprising stories causing the reader to pound the table" and Jingu qiguan 今古奇觀 "Wonderful tales of old and new times". Probably the most important late Ming anecdote writer is Feng Menglong 馮夢龍 who wrote the ghost story Pingyaozhuan 平妖傳 and the collection Xingshi hengyan 醒世恆言 "Proverbs awakening the world" . Apart from short stories, voluminous novels (changpian xiaoshuo 長篇小說) were written that consisted of hundreds of small tales about local and historic heroes: the hero tales Xiyouji 西游記 "Journey to the West" by Wu Cheng'en 吳承恩, Fengshen yanyi 封神演義 "Investiture of the Gods", the Sanguo yanyi 三國演義 "Three Kingdoms", and the Shuihuzhuan 水滸傳 "Water Margin" or "Bandits of Liangshan Swamp", said to be written by Luo Guangzhong 羅貫忠, and finally, the erotic social critic Jin Ping Mei (Jinpingmei) 金瓶梅 "Plums in a golden vase". Theatre plays had been popular since the Song Dynasty, and we possess a collection of famous Yuan theatre plays published during Ming, the Yuanquxuan 元曲選. The greatest Ming theatre play is Tang Xianzu's 湯顯祖 Mudanting 牡丹亭 "Peony Pavillion".